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Discovery of 3-(5'-Substituted)-benzimidazole-5-(1-(3,5-dichloropyridin-4yl)ethoxy)-1H-indazoles as Potent Fibroblast Growth Factor Receptor Inhibitors: Design, Synthesis and Biological Evaluation Wei Yan, Xinyi Wang, Yang Dai, Bin Zhao, Xinying Yang, Jun Fan, Yinglei Gao, Fanwang Meng, Yuming Wang, Cheng Luo, Jing Ai, Mei-Yu Geng, and Wenhu Duan J. Med. Chem., Just Accepted Manuscript • DOI: 10.1021/acs.jmedchem.6b00056 • Publication Date (Web): 27 Jun 2016 Downloaded from http://pubs.acs.org on June 27, 2016

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Journal of Medicinal Chemistry

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Discovery of 3-(5'-Substituted)-benzimidazole-5-(1-(3,5dichloropyridin-4-yl)ethoxy)-1H-indazoles as Potent Fibroblast Growth Factor Receptor Inhibitors: Design, Synthesis and Biological Evaluation Wei Yan,1,# Xinyi Wang,2,6,# Yang Dai,2 Bin Zhao,3 Xinying Yang,2 Jun Fan,3 Yinglei Gao,2 Fanwang Meng,4,5 Yuming Wang,3 Cheng Luo,5 Jing Ai,2,* Meiyu Geng,2,* and Wenhu Duan1,3,* 1

School of Pharmacy, East China University of Science & Technology, 130 Mei Long Road, Shanghai 200237, P.R. China

2

Division of Anti-tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of

Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, P.R. China 3

Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, P.R. China

4

Department of Chemistry, College of Sciences, Shanghai University, 99 Shang Da Road, Shanghai 200444, P.R. China 5

Drug Discovery & Design Center, State Key Laboratory of Drug Research, Shanghai Institute of

Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, P.R. China 1

ACS Paragon Plus Environment

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University of Chinese Academy of Sciences, Beijing, 100049, P.R. China

ABSTRACT

Fibroblast growth factor receptor (FGFR) represents an attractive oncology target for cancer therapy in view of its critical role in promoting cancer formation and progression, as well as causing resistance to approved therapies. In this paper, we describe the identification of the potent pan-FGFR inhibitor (R)21c (FGFR1–4 IC50 values of 0.9, 2.0, 2.0, and 6.1 nM, respectively). Compound (R)-21c exhibited excellent in vitro inhibitory activity against a panel of FGFR-amplified cell lines. Western blot analysis demonstrated that (R)-21c suppressed FGF/FGFR and downstream signaling pathways at nanomolar concentrations. Moreover, (R)-21c provided nearly complete inhibition of tumor growth (96.9% TGI) in NCI-H1581 (FGFR1-amplified) xenograft mice model at the dose of 10 mg/kg/qd via oral administration.

INTRODUCTION

Fibroblast growth factor receptors (FGFRs) are a family of four receptor tyrosine kinases (RTKs), and each of the four FGFRs (FGFR1–4) consists of three extracellular immunoglobulin domains, a single transmembrane domain, and a cytoplasmic tyrosine kinase domain.1 Upon binding to fibroblast growth factors, the receptor undergoes dimerization and autophosphorylation of tyrosine residues on cytoplasmic tail, resulting in activation of downstream signaling including MEK-ERK, PLCγ, and PI3KAkt. Physiologically, FGFR pathway plays important roles in embryogenesis, tissue repair and wound healing.2 FGFR is an oncogenic driver of a broad panel of malignant solid tumors: FGFR1 amplification is identified in about 20% of squamous non-small cell lung carcinoma and about 10% of hormone 2



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receptor-positive breast cancers; FGFR2 is also amplified in about 10% of gastric cancer and 4% of triple-negative breast cancers; mutations of FGFR3 are found in about half of bladder cancers which are strongly related to low-grade tumors; activating mutations of FGFR4 (affecting the kinase domain) are found in 6% to 8% of patients with rhabdomyosarcoma, and overexpression of FGFR4 was found in 50% of hepatocellular carcinomas.3-8 Moreover, aberrant FGFR activation has been associated with poor prognosis and metastatic progression. In addition, over-activation of FGFR signaling is responsible for de novo and acquired resistance to anticancer therapy.9-11 Therefore, the blockade of FGF/FGFR signaling is considered as an attractive approach for the treatment of cancers.

Figure 1. Structures of representative FGFR inhibitors. The early examples of FGFR inhibitors were non-selective. Owing to the high degree of homology of FGFRs with VEGFRs (vascular endothelia growth factor receptors), many compounds developed as FGFR inhibitors also inhibit VEGFR family members at similar potencies, such as 1 (TKI258),12 2 3


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(BIBF-1120),13 and 3 (AZD2171)14 (Figure 1). Although therapies based on inhibiting VEGF/VEGFR signaling pathway have been approved for the treatment of cancers, e.g. 10 (sunitinib),15 11 (sorafenib),16 12 (pazopanib),17 and 13 (vandetanib)18 (Figure 2), undesired side effects such as hypertension and bleeding have been reported.19-21 Recently, medicinal chemists tend to develop more selective FGFR inhibitors, and several orally available FGFR selective inhibitors have been reported to enter clinical trials, for example, 4 (NVP-BGJ398),22 5 (AZD4547),23 6 (CH5183284),24 and 7 (LY2874455)25 (Figure 1). The 3,5-dimethoxy-phenyl moiety of 4 and 5 occupies the same hydrophobic pocket and forms a hydrogen bond with Asp641, which is identified by 8 (PD173074) to contribute to their selectivity for FGFR1;26-27 similar interactions are also observed between 6 and FGFR1.24 Therefore, it is possible that a common single mutation would confer resistance to these inhibitors, which is classified as a category of genetic alteration contributed to the resistance of FGFR inhibitors besides other categories of compensatory pathway activation and epithelial-to-mesenchymal transition, as revealed by limited studies.24, 28-30 As illustrated in the binding model of 7 in the ATP binding site of FGFR3,25 the indazole core binds in the ATP binding pocket and forms two hydrogen bonds with the carbonyl of Glu230 and the NH of Ala232; the vinyl pyrazole fragment extends toward solvent, making important hydrophobic interactions.

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Figure 2. Structures of representative approved VEGFR2 inhibitors. Additionally, a hydrogen bond between the pyridyl nitrogen and Asn236 in hydrophobic pocket is observed; this additional hydrogen bond increases FGFR binding affinity. We envisioned that the interaction between the pyridine fragment and the hydrophobic pocket might overcome the resistance of the former three FGFR selective inhibitors (4, 5, and 6) caused by the single mutation as discussed above. McBride et al. reported compound 9 as a dual FGFR1/VEGFR2 inhibitor (Figure 1);31 this compound showed moderate in vitro and in vivo antitumor efficiency. To understand the ligand-protein interactions, we developed a binding model of compound 9 in the ATP binding site of FGFR1 with a known crystal structure of the FGFR1 kinase domain (PDB ID: 3WJ6).24 As shown in Figure 3, compound 9 binds to the hinge region of the kinase and forms two hydrogen bonds with the carbonyl of Glu562 and the NH of Ala564; an additional hydrogen bond occurs between the carbonyl of Ala564 and N(1)-H of benzimidazole moiety; the benzimidazole moiety extends from the indazole 3-position toward solvent exposed region. In view of the high degree of homology of FGFR1 with FGFR3, it was reasonable to assume that 7 and 9 had similar binding patterns with FGFR in the hinge region and the

5


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solvent exposed region. In view of the importance of the interactions between the pyridine fragment and the surrounded hydrophobic pocket, we envisioned that the introduction of a pyridylalkoxy moiety to the indazole benzimidazole scaffold might form a novel series of FGFR inhibitors with improved potency and selectivity. To test our hypothesis, we designed and synthesized a series of novel 3-benzimidazole5-pyridylalkoxy-1H-indazole derivatives (Figure 4), and these new derivatives displayed excellent in vitro and in vivo antitumor activities. Herein, we report the detailed synthesis and biological evaluation of these compounds.

Figure 3. Proposed binding mode of compound 9 to FGFR1 kinase domain. The atoms of compound 9 are colored as follows: carbon orange, oxygen red, nitrogen blue, fluorine light blue, and hydrogen white. The docked protein structure of FGFR1 is shown in the cartoon and key residues are colored as follows: carbon green, oxygen red, nitrogen blue, and hydrogen white. The hydrogen bonds are colored in black.

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Figure 4. Design of our compounds. RESULTS AND DISCUSSION Lead Optimization and Identification of Compound (R)-21c. To evaluate the aforementioned hypothesis, we prepared compound 14a as the proof-of-concept compound, which possessed moderate enzymatic activity (Table 1). In order to get a putative binding mode, a molecular docking simulation was performed. As depicted in Figure 5, 14a maintained all the critical interactions observed in compounds 7 and 9: the indazole core was anchored to the hinge region of kinase domain via two highly conserved hydrogen bonds with the carbonyl of Glu562 (1.8 Å) and the amino group of Ala564 (2.1 Å); an additional hydrogen bond occurred between the carbonyl of Ala564 and N(1)-H of benzimidazole moiety (2.3 Å); a hydrogen bond between pyridyl nitrogen atom and amino group of Asn568 (2.3 Å) was formed as expected, which reinforced this binding conformation.

7


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Figure 5. Proposed binding mode of compound 14a to FGFR1 kinase domain. The atoms of compound 14a are colored as follows: carbon orange, oxygen red, nitrogen blue, and hydrogen white. The docked protein structure of FGFR1 is shown in the cartoon and key residues are colored as follows: carbon green, oxygen red, nitrogen blue, and hydrogen white. The hydrogen bonds are colored in black. For initial structure-activity relationship exploration, 14a served as a benchmark to analyze both enzymatic and cellular potency contributions from different pyridine ring substitution patterns, and compound 5 was used as the positive control. Despite its moderate potency against FGFR1, 14a displayed a weak inhibitory effect in NCI-H1581 proliferation assay (IC50 of 5016.9 nM). Incorporation of a chlorine atom at the 3-position of the pyridine ring provided 14b, which displayed measurable increases in potencies; when an additional chlorine was introduced to the 5-position, the 3,5-dichloro derivative 14c exhibited a 31-fold increase compared to 14a in cellular potency with an IC50 of 158.7 nM; further introduction of an α-methyl into 14c afforded 15a, which demonstrated a further eleven-fold enhancement of cellular potency compared to 14c (IC50 of 14.1 nM) and 7- and 54-fold increases compared with Table 1. Structure-activity Relationship of Substitutions on Racemic 5-Pyridylalkoxy Group

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Compound

Pyridyl

R

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FGFR1

NCI-H1581 Cell

(IC50, nM)a

(IC50, nM)a

14a

H

20.8 ± 2.3

5016.9 ± 450.0

14b

H

13.6 ± 1.7

3071.1 ± 252.2

14c

H

6.6 ± 0.8

158.7 ± 3.0

14d

H

1.7 ± 0.1

1859.1 ± 156.4

14e

H

4.1 ± 0.8

1232.4 ± 121.7

15a

Me

2.7 ± 0.8

14.1 ± 2.1

15b

Et

5.7 ± 2.3

380.1 ± 21.8

9


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15c

a

Me

22.4 ± 4.2

30.8 ± 4.2

9

–

–

20.3 ± 1.3

749.1 ± 47.2

7

–

–

0.3 ± 0.1

< 0.5

5

–

–

0.6 ± 0.2

92.1 ± 2.8

Values are the mean ± SD of two independent assays.

compound 9 in enzymatic and cellular potencies, respectively. The increases in potency of compounds 14b, 14c, and 15a might be explained by the increased lipophilicity by inclusion of the chlorine atom and the α-methyl.32 The ethyl analogue 15b retained enzymatic potency but turned out to be 27-fold less active than 15a in the NCI-H1581 proliferation assay. Next, we assessed the importance of the position of the pyridine nitrogen by synthesizing compounds 14d and 14e. Interestingly, when pyridine nitrogen was moved to the 2-position, the resulting compound 14d was more potent than the 1- or 3-pyridyl analogues (14a and 14e, respectively). These results implied that the 2-pyridyl isomer interacted in a more favorable manner with the protein; however, when 3,5-dichloro and α-methyl were introduced to 14d, the resulting compound 15c was eight- and two-fold less active than 15a in enzymatic and cellular potencies, respectively. Therefore, 15a with the 3,5-dichloro and α-methyl substitution pattern was chosen as the compound for further optimization. Table 2. Structure-activity Relationship of 3-Heterocycle Substitutions on Racemic 5-(1-(3,5Dichloropyridin-4-yl)ethoxy)-1H-indazole

Compound

R

FGFR1

10


NCI-H1581 Cell


1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

a

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(IC50, nM)a

(IC50, nM)a

16a

1.8 ± 0.1

402.7 ± 13.6

16b

5.1 ± 0.6

3035.7 ± 593.3

16c

228.2 ± 27.1

> 10000

17

2.4 ± 0.6

817.2 ± 13.5


We next turned our attention to the benzimidazole moiety by replacing it with three other heterocyclic bioisosteres. The substituent at the 5’-position was removed for rapid evaluation of the impact of this replacement (Table 2), which led to compound 16a with modest cellular potency. Compared with 16a, benzoxazole analogue 16b displayed three- and eight-fold decreases in enzymatic and cellular potencies, respectively. The decrease in potency of 16b could be explained by the absence of the hydrogen bond formed between benzimidazole NH and Ala564. Replacement of the benzimidazole moiety by benzothiazole completely eroded the cellular activity (16c). Indole analogue 17 retained FGFR activity but was two-fold less active than 16a in NCI-H1581 proliferation assay. These results revealed that the benzimidazole moiety was optimal for FGFR activity. Table 3. Structure-activity Relationship of Substitutions on Benzimidazole

11


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Compound

FGFR1

NCI-H1581 Cell

(IC50, nM)a

(IC50, nM)a

H

1.8 ± 0.1

402.7 ± 13.6

H

16.2 ± 2.4

> 10000

H

> 1000

NTb

4’

5’

16a

H

18a

Me

18b

19a

H

F

2.1 ± 0.4

582.3 ± 66.4

19b

H

Me

2.0 ± 0.1

922.3 ± 94.6

19c

H

OMe

2.8 ± 0.6

315.3 ± 11.7

19d

H

2.1 ± 0.2

5.5 ± 2.4

20

H

1.0 ± 0.1

1.6 ± 1.2

21a

H

0.8 ± 0.1

10.3 ± 0.65

21b

H

1.4 ± 0.1

1.9 ± 0.5

21c

H

1.0 ± 0.2

1.0 ± 0.2

12



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a b

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21d

H

3.6 ± 0.9

5.9 ± 2.9

21e

H

0.2 ± 0.0

2.2 ± 0.5

21f

H

7.6 ± 1.4

8.1 ± 1.1

19e

H

0.4 ± 0.2

0.8 ± 0.1

21g

H

0.3 ± 0.1

1.1 ± 0.2

21h

H

0.6 ± 0.1

1.2 ± 0.6

22

H

1.5 ± 0.1

3.3 ± 1.1

Values are the mean ± SD of two independent assays. Not tested.

Finally, systematic structural optimization of benzimidazole of 16a revealed that substituents on the benzimidazole dramatically impacted FGFR inhibition. As summarized in Table 3, the 4’-methyl analogue 18a showed a nine-fold drop in enzymatic potency compared with 16a and had a cellular IC50 greater than 10000 nM; moreover, the attachment of a 4’-piperidyl group to the benzimidazole moiety (18b) resulted in a significant loss of activity (FGFR1 kinase IC50 greater than 1000 nM). These results revealed that substitution at 4’-position of the benzimidazole moiety was not tolerable. On the contrary, inclusion of substituents at the 5’-position of the benzimidazole had favorable impacts: derivatives bearing hydrophobic groups (such as fluoro, methyl, and methoxyl) retained enzymatic and cellular potencies (compounds 19a–c); moreover, when the hydrophilic methylamino was attached to the 5’position of benzimidazole, the resulting derivative 19d exhibited a cellular potency with an IC50 less 13


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than 10 nM in the NCI-H1581 proliferation assay. Therefore, we introduced a number of amines and alcohol to the 5’-position of the benzimidazole moiety. In general, six-membered ring analogues (20 and 21b–e) had comparable potencies; but 1-ethylpiperazine analogue 21d was nearly four- and six-fold less active than methyl analogue 21c in enzymatic and cellular potencies, respectively; the piperidinylpiperidine analogue 21a had a FGFR1 IC50 of 0.8 nM, but suffered a twelve-fold enzyme-tocell shift, resulting in a cellular IC50 of 10 nM; the homopiperazine analogue 21f was eight-fold less active compared with 21c. The relatively low potency of 21a, 21d, and 21f indicated that the larger ring substitution was less tolerable. Compounds bearing chain substituents (19e, 21g–h, and 22) also turned out to be very potent, and they had comparable potencies to the cyclic amines. As discussed above, a range of functional groups were tolerated at the 5’-position of the benzimidazole moiety, potentially owing to this region extending out of the kinase domain of FGFR1 into a solvent exposed region. Because of the undesired side-effects caused by inhibiting VEGFR2 signaling pathway, five compounds with excellent enzymatic and cellular potencies were selected to be evaluated for their VEGFR2 kinase inhibition. As listed in Table 4, all tested compounds displayed six- to eight-fold selectivity for FGFR1 over VEGFR2, while compound 9 was nearly equipotent against FGFR1 and VEGFR2. This result Table 4. FGFR Selectivity of Selected Compounds FGFR1

VEGFR2

VEGFR2/FGFR1

(IC50, nM)a

(IC50, nM)a

ratio

20

1.0 ± 0.1

7.8 ± 1.3

7.8

21b

1.4 ± 0.1

9.0 ± 1.0

6.4

21c

1.0 ± 0.2

8.0 ± 0.5

8.0

19e

0.4 ± 0.2

2.5 ± 0.5

6.2

Compound

14



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a

22

1.5 ± 0.1

12.6 ± 0.9

8.4

9

20.3 ± 1.3

16.4 ± 0.9

0.8

7

0.3 ± 0.1

5.8 ± 0.4

14.5

5

0.6 ± 0.2

27.0 ± 3.4

45.0

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revealed that incorporation of 5-(1-(3,5-dichloropyridin-4-yl)ethoxyl fragment at the 5-position of the indazole enhanced FGFR inhibitory activity and selectivity over VEGFR2. On the basis of their enzymatic and cellular inhibitory activities, compounds 21c and 22 were chosen for further evaluation. Compounds 21c and 22 were racemates; the enantiomers of 21c and 22 were resolved to evaluate the relative FGFR activity. As illustrated in Figure 6, the R enantiomers were significantly more potent; the result was also consistent with the specific binding revealed in a docking model of compound (R)-21c to FGFR1 (Figure 9, vide infra).

Figure 6. Structures and activities of the enantiomers of 21c and 22. Pharmacokinetic Profiles of Compounds (R)-21c and (R)-22. 15


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Compound (R)-21c or (R)-22 was administrated to male Sprague-Dawley (SD) rats: either as a 1 mg/kg intravenous or orally by gavage at a 5 mg/kg dose and the relevant pharmacokinetic parameters were summarized in Table 5. Both compounds exhibited moderate and similar plasma clearance (2.0 and 1.7 L/h/kg, respectively) and oral exposed (798.6 and 663.9 ng·h/mL, respectively). Compound (R)-22 had a long half-time (7.3 h) but also had a very large volume of distribution (17.6 L/kg) and relatively low oral bioavailability (22%); while (R)-21c had a moderate half-time (2.0 h), volume of distribution (5.8 L/kg), and oral bioavailability (33%). Taking all their data into consideration, we selected compound (R)-21c to further evaluate its in vitro and in vivo antitumor activities. Table 5. Pharmacokinetic Profile of (R)-21c and (R)-22 in Ratsa Dose

Cmax

Tmax

T1/2

AUC0→∞

CL

Vss

F

(mg/kg)

(ng/mL)

(h)

(h)

(ng·h/mL)

(L/h/kg)

(L/kg)

(%)

1 (iv)

300.3

–

2.0

485.3

2.0

5.8

–

5 (po)

97.2

4.0

–

798.6

–

–

33

1 (iv)

735.4

–

7.3

582.3

1.7

17.6

–

5 (po)

195.3

0.8

–

663.9

–

–

22

Compound

(R)-21c

(R)-22 a

Cmax, maximum concentration; Tmax, time of maximum concentration; T1/2, elimination half-life;

AUC0→∞, area under the plasma concentration time curve; CL, clearance; Vss, volume of distribution; F, oral bioavailability. Kinase Inhibition Profile of (R)-21c. By use of an ELISA-based enzymatic assay, (R)-21c was distinguished for its high potency against FGFR1 kinase activity. Then we were prompted to investigate its activity against a panel of tyrosine kinases. Compound (R)-21c showed almost equal potency against FGFR2 and FGFR3, a little weaker against FGFR4, with IC50 values of 2.0, 2.0, and 6.1 nM, respectively, indicating (R)-21c was a pan16



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FGFR inhibitor (Table 6). Compared with compound 5 (FGFR4 IC50 of 165 nM, literature reported data23), (R)-21c was significantly more potent in inhibiting FGFR4, indicating its potential use for the treatment of FGFR4-driven cancer types, for example, hepatocellular carcinoma (HCC).8, 33 Furthermore, (R)-21c was extended to be profiled against a panel of 54 human kinases, including FGFR homologous PDGFR kinase family (PDGFRα, PDGFRβ). Compared to its high potency against FGFR, (R)-21c exhibited much weaker potency against these tested kinases (IC50 >100 nM, or 1000 nM) (Table 6 and Table S1), indicating that (R)-21c was a selective FGFR inhibitor. Table 6. Kinase Inhibition Profile of (R)-21c Tyrosine kinasea

IC50 (nM)b

Tyrosine kinasea

IC50 (nM)b

FGFR1

0.9 ± 0.2

PDGFRβ

> 1000

FGFR2

2.0 ± 0.5

c-Met

> 100

FGFR3

2.0 ± 0.3

Flt1

> 100

FGFR4

6.1 ± 0.4

Flt3

> 100

VEGFR2

7.5 ± 0.8

RET

> 100

EGFR

> 1000

c-Src

> 100

ErbB2

> 1000

Bcr-Abl

> 100

PDGFRα

781.8 ± 7.6

EPHA2

> 100

a

EGFR, epidermal growth factor receptor; PDGFR, platelet derived growth factor receptor; c-Met,

mesenchymal epithelial transition growth factor; Flt, fms-like tyrosine kinase; RET, rearranged during transfection; c-Src, cellular Src kinase; Bcr-Abl, breakpoint cluster region-abelson; EPHA, erythropoietin-producing hepatocellular carcinoma receptor. b

Values are the mean ± SD of three independent assays.

Inhibition on FGFR Signaling of Compound (R)-21c 17


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To further evaluate the cellular activity of (R)-21c targeting FGFR kinase, we analyzed its effects on the phosphorylation of FGFR and its major downstream signaling molecules, PLCγ and Erk. Two representative cancer cell lines with different mechanisms of FGFR activation, FGFR1-fusion protein driven human myeloid leukemia cancer cell line KG-1 and FGFR2-amplified dependent human gastric cancer cell line SNU-16, were chosen. As shown in Figure 7, (R)-21c significantly inhibited the phosphorylation of FGFR1 in a dose dependent manner in KG1 cells. In line with suppressed FGFR1 phosphorylation, the phosphorylation of PLCγ and Erk, the main downstream molecules of FGFR, was also strongly inhibited. Similar results were observed in (R)-21c treated SNU-16 cells. These results suggested that (R)-21c exhibited an effective blockage of FGFRs signaling.

Figure 7. Compound (R)-21c effectively inhibits the phosphorylation of FGFR and the downstream effectors PLCγ and Erk in KG-1 and SNU-16 cells. KG1 (A) or SNU-16 (B) cells treated with (R)-21c for 2 h at the indicated concentrations were lysed and subjected to western blot analysis.

Inhibition on FGFR Signaling-driven cancer cell proliferation of (R)-21c 18



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Increased FGFR signaling promotes cancer cell proliferation. To elucidate the impact of (R)-21c on FGFR mediated cancer cell proliferation, four FGFR-driven cancer cell lines harboring the frequently occurring oncogenic forms of FGFRs were chosen: FGFR1 translocated KG1 cells, FGFR1-amplified NCI-H1581 cells, FGFR2-amplified SNU16 cells, FGFR3-amplified RT112 cells. As shown in Table 7, compound (R)-21c strongly inhibited cell proliferation of KG1, NCI-H1581, SNU16, RT112 cells, with most of the IC50 values of less than 0.1 nM, which was much more potent than that of compound 5, the most advanced pan-FGFR inhibitor in clinical studies.1 These findings suggested that (R)-21c strongly inhibited FGFR-driven cancer cell proliferation via blocking FGFR signaling. Table 7. Antiproliferative Activity of (R)-21c on FGFR Addicted Cell Lines IC50 (nM)a Cell lines

a

(R)-21c

5

KG-1

< 0.1

6.4 ± 1.1

NCI-H1581

4.2 ± 2.5

58.8 ± 1.4

SNU16

< 0.1

13.4 ± 0.3

RT112

< 0.1

88.4 ± 10.5

Values are the mean ± SD of three independent assays.

In Vivo Antitumor Activity of Compound (R)-21c To assess the in vivo antitumor efficacy of (R)-21c, NCI-H1581 xenograft mouse model, which is driven by amplification of FGFR1, was used. Compound (R)-21c was orally administrated once daily at doses of 2 or 10 mg/kg for 21 consecutive days. The results showed that (R)-21c could suppress tumor 19


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growth in a dose-dependent manner, with the tumor growth inhibition rate (TGI) of 44.5% and 96.9% at the doses of 2 mg/kg and 10 mg/kg, respectively, without significant body loss (Figure 8), indicating (R)-21c elicited a robust antitumor efficacy in a FGFR-dependent tumor model. Therefore, (R)-21c was a potential FGFR inhibitor candidate for further drug development.

Figure 8. The inhibitory effect of (R)-21c on tumor growth in NCI-H1581 xenograft model. Compound (R)-21c was administered orally once daily for 21 days. (A) The percentage of tumor growth inhibition values (TGI) was measured on the final day of the study for the drug-treated mice compared with the vehicle control mice: (∗) P< 0.05, (∗) P< 0.01, (∗) P< 0.001, versus vehicle group, using Student’s t test. Results are expressed as the mean ± SEM (n = 6 for inhibitor-treated group, n = 12 for vehicle control group). (B) Body weight measurements during the treatment. Molecular Docking Study of Compound (R)-21c to FGFR1 As illustrated in Figure 9, (R)-21c had a similar binding mode with 14a: the indazole core was anchored to the hinge region of FGFR1 kinase domain via two highly conserved hydrogen bonds with Glu562 and Ala564; a hydrogen bond between pyridyl nitrogen atom and Asn568 was formed as expected. The α-methyl in the linkage between pyridine ring and the indazole core had a favored steric effect: as indicated in Figure 9C, the R-methyl fit in a pocket surrounded by Asp641, Val492, and 20



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Glu485, thus compelling the pyridine ring to form a strong hydrogen bond with Asn568; on the contrary, an S-methyl would have an unfavored steric hindrance effect with Val492 which would destabilize the active conformation. The benzimidazole moiety was located in a narrow hydrophobic cleft that was formed by five residues (namely, Leu484, Tyr563, Ala564, Ser565, and Gly567): an additional hydrogen bond occurred between the carbonyl of Ala564 and N(1)-H of benzimidazole moiety that reinforced this binding conformation; the 4’-position of benzimidazole was surrounded by Leu484, Ser565, and Gly567; while the 5’-substitution extended out of this pocket into the solvent exposed region; this binding information explained why 4’-substitution of benzimidazole was not tolerable, but a range of functional groups were tolerated at the 5’-position.

Figure 9. The proposed binding mode of (R)-21c with FGFR1. (A) The atoms of (R)-21c are colored as follows: carbon orange, oxygen red, nitrogen blue, chlorine green, and hydrogen white. The docked protein structure of FGFR1 is shown in the cartoon and key residues are colored as follows: carbon green, oxygen red, nitrogen blue, and hydrogen white. The hydrogen bonds are colored in black. (B) The docked protein structure of FGFR1 is shown in surface. The surfaces of Gly485 and Glu486 are omitted for clarity. (C) The R-methyl fit in a pocket surrounded by three residues (Asp641, Val492, and Glu485).

CHEMISTRY 21


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Scheme 1a

a

Reagents and conditions: (a) 5-hydroxyindole, Cs2CO3, DMF, 70 °C; (b) NaNO2, HCl, H2O/dioxane, 0 °C to rt; (c) Et3N, piperidine, NMP, 120 °C; (d) H2, 10% Pd/C, MeOH, rt; (e) S8, DMF, 90 °C. As outlined in Schemes 1–2, benzyl chlorides 23 or methane sulfonates 31 were reacted with 5hydroxy-1H-indole to provide ethers 24 or 32, which were transformed to 3-carbaldehyde-1H-indazoles 25 or 33 by treatment of dilute nitrous acid.34 Nucleophilic displacement of the C-5 fluorine of 26a with piperidine afforded 27. Reduction of 27 with hydrogen afforded diamine 28 which should be protected in argon atmosphere during workup and reacted immediately after workup with aldehydes 25 or 33 to afford compounds 14 and 15. Compounds 16a and 16c were prepared by analogous methods (Scheme 3); while the stronger oxidant DDQ rather than sulfur was used in the final cyclo-condensation step in the preparation of 16b. The indole-indazole derivative 17 was synthesized via palladium-catalyzed cross-coupling reaction of iodide 35 and boronic acid 36; compounds 35 and 36 were prepared according to literature procedures.35-36

Scheme 2a 22



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a

Reagents and conditions: (a) for 30a and 30c, LDA, acetaldehyde, THF, −78 °C; for 30b, LDA, propionaldehyde, THF, −78 °C; (b) MsCl, Et3N, CH2Cl2, 0 °C to rt; (c) 5-hydroxyindole, Cs2CO3, DMF, 70 °C; (d) NaNO2, HCl, H2O/dioxane, 0 °C to rt; (e) 28, S8, DMF, 90 °C. Scheme 3a

a

Reagents and conditions: (a) for 16a and 16c, S8, DMF, 90 °C; for 16b, (i) DMF, 90 °C; (ii) DDQ, CHCl3, reflux; (b) (i) Cs2CO3, Pd(dppf)2Cl2, dioxane, 90 °C; (ii) 4 N HCl in MeOH. Compounds 18–22 were prepared via a similar route (Scheme 4). An array of 2-nitroaniline intermediates (40) were prepared starting from 26a by displacement of fluorine with commercial available amines (39). Acylation of amine 19d with bromoacetyl chloride followed by displacement of 23


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the bromine with dimethylamine furnished amide 19e. Intermediates 38 and 41 were prepared according to literature procedures.37-38 Scheme 4a

a

Reagents and conditions: (a) (i) H2, 10% Pd/C, MeOH, rt; (ii) 33a, S8, DMF, 90 °C; (b) for 26d, methylammonium chloride, DIPEA, NMP, 140 °C; for 40, DIPEA, NMP, 120 °C; (c) (i) 2-bromoacetyl chloride, CH2Cl2, rt; (ii) dimethylamine, THF, rt.

24



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The enantiomers of 21c and 22 were resolved to evaluate the relative FGFR activities. The racemic alcohol 30a was reacted with chiral acid 42 via kinetic resolution reaction (twice) to give (S)-30a with an enantiomeric excess (ee) of 98% (Scheme 5).39 Mitsunobu reaction of (S)-30a with acetic acid followed by hydrolysis with sodium hydroxide afforded (R)-30a in nearly complete configuration inversion (ee 97%). Compound (R)-21c was prepared starting from (S)-30a in a similar manner as described for the racemic 21c (Scheme 6). It was noted that partial racemization was observed in the SN2 ether formation step, and the ee of (R)-32a was 89%; the corresponding aldehyde was suspended in ethyl acetate and filtered to generate enantiomerically pure (R)-33a with an ee of over 99%. Scheme 5a

a

Reagents and conditions: (a) (i) DCC, 4-DMAP, toluene, 0 °C; (ii) NaOH, H2O, EtOH, rt; (b) (i) HOAc, DIAD, PPh3, THF, 0 °C to rt; (ii) NaOH, H2O, EtOH, rt. CONCLUSION In

summary,

we

have

developed

a

series

of

3-(5'-substituted)-benzimidazole-5-(1-(3,5-

dichloropyridin-4-yl)ethoxy)-1H-indazoles as potent FGFR inhibitors. Structural optimization of 14a led to the identification of (R)-21c, which had pan-FGFR inhibitory activities against FGFR1–4 (IC50 values of 0.9, 2.0, 2.0, and 6.1 nM, respectively) and eight-fold selectivity over VEGFR2. Compared with other FGFR selective inhibitors, (R)-21c potently inhibited FGFR4, indicating its potential use for the treatment of FGFR4-driven cancer types. Western blot analysis revealed that (R)-21c suppressed FGF/FGFR and downstream signaling pathways at nanomolar concentrations. Furthermore, (R)-21c displayed potent antiproliferative effect against a number of FGFR-amplified cell lines including NCI25


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H1581, KG1, SNU16, and RT112. After an oral administration of compound (R)-21c at a dose of 10 mg/kg/qd, almost complete tumor stasis was observed in nude mice bearing NCI-H1581 human lung cancer xenograft after 21 days of initial administration, indicating that (R)-21c was a potential FGFR inhibitor for further drug development. Scheme 6a

a

Reagents and conditions: (a) MsCl, Et3N, CH2Cl2, 0 °C to rt; (b) 5-hydroxyindole, Cs2CO3, DMF, 70 °C; (c) NaNO2, HCl, H2O/dioxane, 0 °C to rt; (d) (i) 40c, H2, 10% Pd/C, MeOH, rt; (ii) S8, DMF, 90 °C. EXPERIMENTAL SECTION Chemistry. All starting materials and reagents were either obtained from commercial suppliers or prepared according to literature reported procedures. All purchased chemicals and solvents were used without further purification unless otherwise noted. Flash chromatography was performed using silica gel (300−400 mesh). All reactions were monitored by thin-layer chromatography (TLC), using silica gel plates with fluorescence F254 and visualized under UV light. 1H NMR spectral data were recorded on Varian Mercury 300 or 400 NMR spectrometer, and 13C NMR was recorded on Varian Mercury 126 or 26



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Page 28 of 71

151 NMR spectrometer at ambient temperature. Chemicals shifts (δ) were reported in parts per million, coupling constants (J) values were in hertz, and the splitting patterns were abbreviated as follows: s for singlet; d for doublet; t for triplet; q for quartet and m for multiplet. The low or high resolution of EI-MS was recorded on a Finnigan/MAT95 spectrometer. All tested compounds were purified to ≥95% purity as determined by high performance liquid chromatography (HPLC).

General procedure A: Synthesis of target compounds 14–15, 16a and 16c. A mixture of the aldehyde (25a–e or 33a–c) (0.3 mmol), aniline (28, 34a or 34c) (0.3 mmol), and sulfur (0.6 mmol) was heated to 90 °C for 2 h under argon atmosphere40. Ethyl acetate was added and the reaction mixture was partitioned between ethyl acetate and water. The organic layer was washed with water and brine successively, dried over anhydrous sodium sulfate, and concentrated in vacuum. The resulting residue was purified by silica gel chromatography (dichloromethane/methanol + 2% of aqueous ammonia, v/v, 99:1 to 97:3) to give the desired product.

3-(5-(Piperidin-1-yl)-1H-benzo[d]imidazol-2-yl)-5-(pyridin-4-ylmethoxy)-1H-indazole (14a). The title compound was prepared from 25a and 28 following general procedure A. Yellow solid (56%), mp 232 °C dec. 1H NMR (300 MHz, CD3OD) δ 8.54 (dd, J = 4.6, 1.6 Hz, 2H), 8.00 (d, J = 2.0 Hz, 1H), 7.57 (dd, J = 19.5, 7.6 Hz, 4H), 7.25 (dd, J = 9.1, 2.4 Hz, 2H), 7.08 (dd, J = 8.8, 2.1 Hz, 1H), 5.31 (s, 2H), 3.19–3.08 (m, 4H), 1.87–1.71 (m, 4H), 1.66–1.55 (m, 2H).

13

C NMR (126 MHz, acetone-d6) δ

155.1, 152.1, 150.8 (2C), 150.5, 147.3, 139.9, 138.7, 137.5, 136.0, 122.7 (2C), 122.7, 120.1, 115.5, 112.3, 104.3, 103.1, 69.4, 53.2 (2C), 27.0 (2C), 25.1. HRMS (EI+) m/z calcd for C25H24N6O 424.2012; found 424.2011.

5-((3-Chloropyridin-4-yl)methoxy)-3-(5-(piperidin-1-yl)-1H-benzo[d]imidazol-2-yl)-1H-indazole (14b). The title compound was prepared from 25b and 28 following general procedure A. Yellow solid 27


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(50%), mp 140–142 °C. 1H NMR (300 MHz, CD3OD) δ 8.59 (s, 1H), 8.51 (d, J = 5.0 Hz, 1H), 8.03 (s, 1H), 7.76 (d, J = 4.9 Hz, 1H), 7.58 (d, J = 3.6 Hz, 1H), 7.55 (d, J = 3.9 Hz, 1H), 7.30–7.23 (m, 2H), 7.10 (d, J = 8.8 Hz, 1H), 5.37 (s, 2H), 3.22–3.13 (m, 4H), 1.85–1.75 (m, 4H), 1.67–1.58 (m, 2H). 13C NMR (151 MHz, acetone-d6) δ 154.8, 149.8, 149.2, 147.6, 144.8, 139.9, 138.8, 138.6, 137.4, 130.8, 123.9, 122.6, 120.0 (2C), 116.2, 112.4, 104.5, 100.0, 67.1, 53.4 (2C), 26.8 (2C), 24.9. HRMS (EI+) m/z calcd for C25H23ClN6O 458.1622; found 458.1619.

5-((3,5-Dichloropyridin-4-yl)methoxy)-3-(5-(piperidin-1-yl)-1H-benzo[d]imidazol-2-yl)-1Hindazole (14c). The title compound was prepared from 25c and 28 following general procedure A. Yellow solid (72%), mp 205 °C dec. 1H NMR (300 MHz, CD3OD) δ 8.61 (s, 2H), 8.11 (d, J = 2.2 Hz, 1H), 7.64–7.50 (m, 2H), 7.30 (s, 1H), 7.19–7.09 (m, 2H), 5.45 (s, 2H), 3.26–3.14 (m, 4H), 1.89–1.75 (m, 4H), 1.68–1.57 (m, 2H).

13

C NMR (126 MHz, acetone-d6) δ 155.3, 149.9 (2C), 148.9, 147.7, 141.2,

138.9, 137.3, 134.3 (2C), 122.6, 120.2, 116.3, 112.5, 104.3, 98.9, 65.5, 53.5 (2C), 26.7 (2C), 24.8. HRMS (EI+) m/z calcd for C25H22Cl2N6O 492.1232; found 492.1232.

3-(5-(Piperidin-1-yl)-1H-benzo[d]imidazol-2-yl)-5-(pyridin-3-ylmethoxy)-1H-indazole (14d). The title compound was prepared from 25d and 28 following general procedure A. Yellow solid (54%), mp 152–154 °C. 1H NMR (300 MHz, CD3OD) δ 8.72 (s, 1H), 8.51 (d, J = 5.0 Hz, 1H), 8.08–7.97 (m, 2H), 7.63–7.45 (m, 3H), 7.28 (s, 1H), 7.22 (dd, J = 9.1, 2.2 Hz, 1H), 7.12 (dd, J = 8.8, 2.1 Hz, 1H), 5.30 (s, 2H), 3.24–3.15 (m, 4H), 1.86–1.74 (m, 4H), 1.69–1.57 (m, 2H).

13

C NMR (126 MHz, acetone-d6) δ

155.3, 150.5, 150.3, 150.2, 147.7, 138.6, 137.5, 136.4, 133.9, 124.3, 122.7, 120.3, 116.2, 112.3, 104.1, 102.5, 68.8, 53.2 (2C), 27.0 (2C), 25.1. HRMS (EI+) m/z calcd for C25H24N6O 424.2012; found 424.2004.

28



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3-(5-(Piperidin-1-yl)-1H-benzo[d]imidazol-2-yl)-5-(pyridin-2-ylmethoxy)-1H-indazole (14e). The title compound was prepared from 25e and 28 following general procedure A. Yellow solid (61%), mp 159–160 °C. 1H NMR (300 MHz, CD3OD) δ 8.57 (d, J = 4.9 Hz, 1H), 8.02 (d, J = 2.0 Hz, 1H), 7.90 (td, J = 7.7, 1.7 Hz, 1H), 7.70 (d, J = 7.9 Hz, 1H), 7.62–7.50 (m, 2H), 7.44–7.35 (m, 1H), 7.29–7.21 (m, 2H), 7.11 (dd, J = 8.8, 2.2 Hz, 1H), 5.32 (s, 2H), 3.25–3.11 (m, 4H), 1.89–1.74 (m, 4H), 1.69–1.56 (m, 2H).

13

C NMR (126 MHz, acetone-d6) δ 158.4, 155.3, 150.1, 147.8, 138.6, 137.5, 137.3, 123.6, 122.8,

122.2, 120.1, 116.2, 112.3, 104.3, 101.7, 72.1, 53.5 (2C), 26.8 (2C), 24.9. HRMS (EI+) m/z calcd for C25H24N6O 424.2012; found 424.2020.

5-(1-(3,5-Dichloropyridin-4-yl)ethoxy)-3-(5-(piperidin-1-yl)-1H-benzo[d]imidazol-2-yl)-1Hindazole (15a). The title compound was prepared from 33a and 28 following general procedure A. Yellow solid (70%), mp 202 °C dec. 1H NMR (300 MHz, acetone-d6) δ 12.40 (s, 1H), 11.48 (s, 1H), 8.51 (s, 2H), 8.03 (s, 1H), 7.64 (s, 1H), 7.52 (d, J = 9.0 Hz, 1H), 7.18 (dd, J = 9.2, 1.9 Hz, 1H), 7.11– 6.97 (m, 2H), 6.19 (q, J = 6.7 Hz, 1H), 3.22–3.08 (m, 4H), 1.85 (d, J = 6.6 Hz, 3H), 1.81–1.69 (m, 4H), 1.65–1.55 (m, 2H).

13

C NMR (126 MHz, acetone-d6) δ 153.3, 149.7 (2C), 145.2, 141.3, 138.5, 137.5,

136.4, 132.0 (2C), 122.7, 120.3, 120.2, 115.5, 112.2, 105.1, 99.0, 72.9, 53.1 (2C), 27.0 (2C), 25.1, 19.0. HRMS (EI+) m/z calcd for C26H24Cl2N6O 506.1389; found 506.1390.

5-(1-(3,5-Dichloropyridin-4-yl)propoxy)-3-(5-(piperidin-1-yl)-1H-benzo[d]imidazol-2-yl)-1Hindazole (15b). The title compound was prepared from 33b and 28 following general procedure A. Yellow solid (57%), mp 170 °C dec. 1H NMR (400 MHz, CD3OD) δ 8.41 (s, 2H), 7.84 (d, J = 2.1 Hz, 1H), 7.57 (d, J = 8.8 Hz, 1H), 7.46 (d, J = 9.0 Hz, 1H), 7.25 (s, 1H), 7.16 (dd, J = 9.0, 1.7 Hz, 1H), 7.09 (dd, J = 8.8, 2.0 Hz, 1H), 6.04–5.90 (m, 1H), 3.23–3.05 (m, 4H), 2.46–2.27 (m, 1H), 2.16–2.01 (m, 1H),

29


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1.89–1.70 (m, 4H), 1.60 (d, J = 5.0 Hz, 2H), 1.13 (t, J = 7.4 Hz, 3H). HRMS (EI+) m/z calcd for C27H26Cl2N6O 520.1545; found 520.1544.

5-(1-(2,4-Dichloropyridin-3-yl)ethoxy)-3-(5-(piperidin-1-yl)-1H-benzo[d]imidazol-2-yl)-1Hindazole (15c). The title compound was prepared from 33c and 28 following general procedure A. Beige solid (40%), mp 174 °C dec. 1H NMR (300 MHz, CD3OD) δ 8.12 (d, J = 5.3 Hz, 1H), 7.85 (d, J = 2.0 Hz, 1H), 7.57 (d, J = 8.4 Hz, 1H), 7.47 (d, J = 9.0 Hz, 1H), 7.39 (d, J = 5.1 Hz, 1H), 7.23 (s, 1H), 7.17 (dd, J = 9.0, 2.3 Hz, 1H), 7.09 (d, J = 8.6 Hz, 1H), 6.26 (q, J = 6.6 Hz, 1H), 3.21–3.12 (m, 3H), 1.89–1.75 (m, 6H), 1.69–1.57 (m, 2H).

13

C NMR (126 MHz, acetone-d6) δ 153.4, 149.6 (2C), 145.3,

145.1, 138.9, 137.5, 137.2, 136.3, 132.1 (2C), 124.6, 123.0, 122.7, 120.2, 112.1, 107.9, 107.64, 103.9, 73.9, 51.8 (2C), 26.9 (2C), 25.6, 18.6. HRMS (EI+) m/z calcd for C26H24Cl2N6O 506.1389; found 506.1385.

3-(1H-Benzo[d]imidazol-2-yl)-5-(1-(3,5-dichloropyridin-4-yl)ethoxy)-1H-indazole (16a). The title compound was prepared from 33a and o-phenylenediamine (34a) following general procedure A. White solid (79%), mp 222 °C dec. 1H NMR (300 MHz, DMSO-d6) δ 13.48 (s, 1H), 12.86 (s, 1H), 8.61 (s, 2H), 7.83 (d, J = 2.3 Hz, 1H), 7.78–7.72 (m, 1H), 7.55 (d, J = 9.0 Hz, 1H), 7.51–7.45 (m, 1H), 7.26– 7.19 (m, 2H), 7.16 (dd, J = 9.0, 2.4 Hz, 1H), 6.10 (q, J = 6.6 Hz, 1H), 1.78 (d, J = 6.6 Hz, 3H). 13C NMR (126 MHz, acetone-d6) δ 153.5, 149.7 (2C), 148.2, 145.6, 145.2, 138.5, 137.1, 135.1, 132.0 (2C), 123.5, 122.8, 122.4, 120.4, 120.2, 112.4, 111.9, 104.8, 72.9, 19.1. HRMS (EI+) m/z calcd for C21H15Cl2N5O 423.0654; found 423.0653.

Synthesis of 2-(5-(1-(3,5-dichloropyridin-4-yl)ethoxy)-1H-indazol-3-yl)benzo[d]oxazole (16b). Compound 33a (100 mg, 0.3 mmol) and 2-aminophenol (34b) (36 mg, 0.3 mmol) were dissolved in N,N-dimethylformamide (3 mL) and heated to 100 °C for 2 h. The mixture was concentrated to dryness 30



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Page 32 of 71

and dissolved in chloroform (2 mL). 2,3-Dichloro-5,6-dicyano-1,4-benzoquinone (150 mg, 0.66 mmol) was added and the solution was heated to reflux for 2 h.41 The reaction mixture was diluted by chloroform and washed with water and brine successively, dried over anhydrous sodium sulfate, and concentrated in vacuum. The resulting residue was purified by silica gel chromatography (dichloromethane/methanol, v/v, 98:2) to give the title product as a yellow solid (80 mg, 63%), mp 232 °C dec. 1H NMR (300 MHz, CDCl3) δ 12.39 (s, 1H), 8.44 (s, 2H), 7.87–7.80 (m, 1H), 7.71 (d, J = 2.0 Hz, 1H), 7.65–7.60 (m, 1H), 7.57 (d, J = 9.1 Hz, 1H), 7.46–7.36 (m, 2H), 7.20 (dd, J = 9.1, 2.4 Hz, 1H), 6.17 (q, J = 6.7Hz, 1H), 1.85 (d, J = 6.7 Hz, 3H).

13

C NMR (126 MHz, acetone-d6) δ 159.5, 154.2,

151.0, 149.8 (2C), 145.0, 143.0, 138.3, 133.7, 132.0 (2C), 126.1, 125.6, 123.5, 120.8, 113.0, 111.5, 103.6, 73.0, 19.0. HRMS (EI+) m/z calcd for C21H14Cl2N4O2 424.0494; found 424.0503.

2-(5-(1-(3,5-Dichloropyridin-4-yl)ethoxy)-1H-indazol-3-yl)benzo[d]thiazole

(16c).

The

title

compound was prepared from 33a and 2-aminobenzenethiol (34c) following general procedure A. Beige solid (35%), mp 220 °C dec. 1H NMR (300 MHz, acetone-d6) δ 12.69 (s, 1H), 8.55 (s, 2H), 8.21 (d, J = 8.6 Hz, 1H), 8.07 (d, J = 8.0 Hz, 1H), 7.85 (d, J = 2.3 Hz, 1H), 7.65–7.55 (m, 2H), 7.46 (t, J = 7.6 Hz, 1H), 7.24 (dd, J = 9.0, 2.5 Hz, 1H), 6.20 (q, J = 6.7 Hz, 1H), 1.86 (d, J = 6.7 Hz, 3H). 13C NMR (126 MHz, acetone-d6) δ 162.9, 155.2, 154.2, 149.7 (2C), 145.1, 140.0, 138.8, 134.9, 131.9 (2C), 127.1, 126.2, 123.8, 122.7, 122.0, 121.0, 112.9, 103.6, 72.8, 19.1. HRMS (EI+) m/z calcd for C21H14Cl2N4OS 440.0265; found 440.0262.

Synthesis

of

5-(1-(3,5-dichloropyridin-4-yl)ethoxy)-3-(1H-indol-2-yl)-1H-indazole

(17).

Compounds 35 (72 mg, 0.14 mmol) and 36 (40 mg, 0.15 mmol) were dissolved in dioxane (5 mL) and cesium carbonate (91 mg, 0.28 mmol) was added. The suspension was degassed under argon bubbling for 10 min before Pd(dppf)2Cl2 (7 mg, 0.01 mmol) was added. The reaction mixture was heated to 90 °C 31


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for 2 h and then diluted with ethyl acetate. The solution was washed with water and brine successively, dried over anhydrous sodium sulfate, and concentrated in vacuum. The resulting residue was dissolved in a solution of hydrochloric acid in methanol (0.5 mL, 4 N) and the mixture was continually stirred overnight at room temperature. The mixture was concentrated and purified by silica gel chromatography (dichloromethane/methanol, v/v, 98:2) to give the title product as a light brown solid (34 mg, 58%), mp 216 °C dec. 1H NMR (400 MHz, CDCl3) δ 9.96 (s, 1H), 9.05 (s, 1H), 8.45 (s, 2H), 7.71 (d, J = 7.5 Hz, 1H), 7.43–7.36 (m, 2H), 7.30 (s, 1H), 7.25–7.21 (m, 1H), 7.20–7.13 (m, 2H), 6.97 (s, 1H), 6.14 (q, J = 6.8 Hz, 1H), 1.86 (d, J = 6.7 Hz, 3H). 13C NMR (126 MHz, CDCl3) δ 152.5, 149.1 (2C), 144.4, 138.8, 137.7, 136.0, 131.3 (2C), 131.0, 129.2, 122.9, 120.8, 120.2, 119.9, 111.3, 111.0, 102.8, 100.9, 72.2, 18.9. HRMS (EI+) m/z calcd for C22H16Cl2N4O 422.0701; found 422.0701. General procedure B: Synthesis of target compounds 18–22. The substituted 2-nitroaniline (26, 37– 38 or 40–41) (0.3 mmol) was dissolved in methanol (3 mL) and 10% Pd/C (0.03 mmol) was added. The mixture was stirred at room temperature under hydrogen atmosphere for 2 h. The mixture was filtered and the filtrate was concentrated to dryness and dissolved in N,N-dimethylformamide (3 mL). Compound 33a (0.3 mmol) and sulfur (0.6 mmol) was added. The mixture was heated to 90 °C for 2 h under argon atmosphere. Ethyl acetate was added and the reaction mixture was partitioned between ethyl acetate and water. The organic layer was washed with water and brine successively, dried over anhydrous sodium sulfate, and concentrated in vacuum. The resulting residue was purified by silica gel chromatography (dichloromethane/methanol + 2% of aqueous ammonia, v/v, 99:1 to 95:5) to give the desired product.

5-(1-(3,5-Dichloropyridin-4-yl)ethoxy)-3-(4-methyl-1H-benzo[d]imidazol-2-yl)-1H-indazole (18a). The title compound was prepared from 37a following general procedure B. Beige solid (51%), 32



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mp 137–139 °C. 1H NMR (300 MHz, CD3OD) δ 8.42 (s, 2H), 7.73 (s, 1H), 7.49 (d, J = 9.0 Hz, 1H), 7.36 (s, 1H), 7.23–7.12 (m, 2H), 7.05 (d, J = 7.2 Hz, 1H), 6.21 (q, J = 6.7 Hz, 1H), 2.74–2.62 (m, 3H), 1.82 (d, J = 6.7 Hz, 3H).

5-(1-(3,5-Dichloropyridin-4-yl)ethoxy)-3-(4-(piperidin-1-yl)-1H-benzo[d]imidazol-2-yl)-1Hindazole (18b). The title compound was prepared from 37b following general procedure B. Brown solid (43%), mp 120–122 °C. 1H NMR (300 MHz, DMSO-d6) δ 13.45 (s, 1H), 12.76 (s, 1H), 8.56 (s, 2H), 8.08 (s, 1H), 7.54 (d, J = 9.1 Hz, 1H), 7.20 (d, J = 8.7 Hz, 1H), 7.05 (t, J = 7.7 Hz, 1H), 6.98 (d, J = 7.7 Hz, 1H), 6.53 (d, J = 7.5 Hz, 1H), 6.20 (dd, J = 12.6, 6.4 Hz, 1H), 3.72–3.50 (m, 4H), 1.90–1.72 (m, 7H), 1.68–1.66 (m, 2H). 13C NMR (126 MHz, CD3OD) δ 154.0, 149.7 (2C), 147.0, 146.2, 139.2, 138.3, 137.0, 132.8 (2C), 130.3, 124.5, 122.9, 120.9, 112.4, 110.7, 106.7, 74.2, 53.6 (2C), 27.1 (2C), 25.5, 18.7. HRMS (EI+) m/z calcd for C26H24Cl2N6O 506.1389; found 506.1387.

5-(1-(3,5-Dichloropyridin-4-yl)ethoxy)-3-(5-fluoro-1H-benzo[d]imidazol-2-yl)-1H-indazole (19a). The title compound was prepared from 26a following general procedure B. White solid (72%), mp >250 °C. 1H NMR (300 MHz, DMSO-d6) δ 13.53–13.51 (m, 1H), 12.99 (s, 1H), 8.62–8.61 (m, 2H), 7.78 (s, 1H), 7.74–7.43 (m, 1H), 7.55 (d, J = 8.1 Hz, 1H), 7.51–7.19 (m, 1H), 7.16 (dd, J = 9.0, 2.4 Hz, 1H), 7.11–7.04 (m,1H), 6.10 (q, J = 6.7 Hz, 1H), 1.78 (d, J = 6.7 Hz, 3H). HRMS (EI+) m/z calcd for C21H14Cl2FN5O 441.0559; found 441.0562.

5-(1-(3,5-Dichloropyridin-4-yl)ethoxy)-3-(5-methyl-1H-benzo[d]imidazol-2-yl)-1H-indazole (19b). The title compound was prepared from 26b following general procedure B. White solid (55%), mp 215 °C dec. 1H NMR (300 MHz, CD3OD) δ 8.43 (s, 2H), 7.81 (s, 1H), 7.67–7.32 (m, 3H), 7.17 (dd, J = 9.0, 2.1 Hz, 1H), 7.11 (d, J = 7.8 Hz, 1H), 6.24 (q, J = 6.6 Hz, 1H), 2.50 (s, 3H), 1.83 (d, J = 6.6 Hz, 3H). 13C NMR (126 MHz, CD3OD) δ 154.1, 149.8 (2C), 148.5, 146.3, 139.1, 136.9, 133.7, 132.7 (2C), 33


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125.2, 122.7, 120.9, 116.0, 112.5, 104.87, 73.65, 21.78, 18.92. HRMS (EI+) m/z calcd for C22H17Cl2N5O 437.0810; found 437.0810.

5-(1-(3,5-Dichloropyridin-4-yl)ethoxy)-3-(5-methoxy-1H-benzo[d]imidazol-2-yl)-1H-indazole (19c). The title compound was prepared from 26c following general procedure B. Yellow solid (58%), mp 150 °C dec. 1H NMR (300 MHz, CD3OD) δ 8.43 (s, 2H), 7.81 (d, J = 1.9 Hz, 1H), 7.55 (d, J = 8.8 Hz, 1H), 7.47 (d, J = 9.0 Hz, 1H), 7.21–7.12 (m, 2H), 6.92 (dd, J = 8.8, 2.3 Hz, 1H), 6.23 (q, J = 6.5 Hz, 1H), 3.88 (s, 3H), 1.83 (d, J = 6.6 Hz, 3H). HRMS (EI+) m/z calcd for C22H17Cl2N5O2 453.0759; found 453.0751.

2-(5-(1-(3,5-Dichloropyridin-4-yl)ethoxy)-1H-indazol-3-yl)-N-methyl-1H-benzo[d]imidazol-5amine (19d). The title compound was prepared from 26d following general procedure B. Yellow solid (62%), mp 182 °C dec. 1H NMR (300 MHz, DMSO-d6) δ 13.29 (s, 1H), 12.29 (s, 1H), 8.60 (s, 2H), 7.81 (s, 1H), 7.50 (d, J = 9.0 Hz, 1H), 7.41 (s, 1H), 7.12 (dd, J = 9.0, 2.4 Hz, 1H), 6.58 (dd, J = 8.7, 2.0 Hz, 1H), 6.49 (s, 1H), 6.08 (q, J = 6.7 Hz, 1H), 5.61 (s, 1H), 2.73 (s, 3H), 1.78 (d, J = 6.7 Hz, 3H). 13C NMR (126 MHz, acetone-d6) δ 153.3, 149.6 (2C), 147.8, 145.9, 145.3, 138.5, 137.4, 132.0 (2C), 122.5, 120.2, 118.5, 112.1, 112.0, 105.2, 94.7, 73.0, 31.4, 19.0. HRMS (EI+) m/z calcd for C22H18Cl2N6O 452.0919; found 452.0907.

N-(2-(5-(1-(3,5-Dichloropyridin-4-yl)ethoxy)-1H-indazol-3-yl)-1H-benzo[d]imidazol-6-yl)-2(dimethylamino)-N-methylacetamide (19e). To a mixture of 19d (50 mg, 0.11 mmol) and triethylamine (30 µL, 0.22 mmol) in N,N-dimethylformamide (2 mL), 2-bromoacetyl chloride (10 µL, 0.13 mmol) was added dropwise at 0 °C. The reaction mixture was stirred at room temperature for 3 h and concentrated before a solution of dimethylamine in THF (5 mL, 2 N) was added. The mixture was stirred overnight at room temperature and was concentrated. The resulting residue was purified by silica 34



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gel chromatography (dichloromethane/methanol + 2% of aqueous ammonia, v/v, 96:4) to give the title compound as a beige solid (26 mg, 45%), mp 185 °C dec. 1H NMR (300 MHz, CD3OD) δ 8.45 (s, 2H), 7.83 (s, 1H), 7.73 (s, 1H), 7.56 (s, 1H), 7.50 (d, J = 9.1 Hz, 1H), 7.24–7.13 (m, 2H), 6.23 (q, J = 6.7 Hz, 1H), 3.35 (s, 3H), 3.03 (s, 2H), 2.25 (s, 6H), 1.84 (d, J = 6.7 Hz, 3H). HRMS (EI+) m/z calcd for C26H25Cl2N7O2 537.1447; found 537.1454.

5-(1-(3,5-Dichloropyridin-4-yl)ethoxy)-3-(5-(1-methylpiperidin-4-yl)-1H-benzo[d]imidazol-2-yl)1H-indazole (20). The title compound was prepared from 38 following general procedure B. Beige solid (49%), mp 162–163 °C. 1H NMR (300 MHz, CD3OD) δ 8.43 (s, 2H), 7.83 (d, J = 1.4 Hz, 1H), 7.58 (s, 1H), 7.56–7.44 (m, 2H), 7.23–7.13 (m, 2H), 6.23 (q, J = 6.6 Hz, 1H), 3.04 (d, J = 10.9 Hz, 2H), 2.76– 2.63 (m, 1H), 2.35 (s, 3H), 2.29–2.14 (m, 2H), 2.00–1.78 (m, 7H).

13

C NMR (126 MHz, CD3OD) δ

154.1, 149.8 (2C), 148.9, 146.3, 142.4, 139.1, 136.8, 132.7 (2C), 123.2, 122.8, 120.9, 116.1, 112.5, 104.9, 73.7, 57.3 (2C), 46.4, 43.2, 34.7 (2C), 18.9. HRMS (EI+) m/z calcd for C27H26Cl2N6O 520.1545; found 520.1550.

3-(5-([1,4'-Bipiperidin]-1'-yl)-1H-benzo[d]imidazol-2-yl)-5-(1-(3,5-dichloropyridin-4-yl)ethoxy)1H-indazole (21a). The title compound was prepared from 40a following general procedure B. Yellow solid (45%), mp 185 °C dec. 1H NMR (300 MHz, CD3OD) δ 8.43 (s, 2H), 7.83 (s, 1H), 7.56 (d, J = 9.4 Hz, 1H), 7.47 (d, J = 9.2 Hz, 1H), 7.18–7.14 (m, 2H), 7.07 (d, J = 9.0 Hz, 1H), 6.24 (q, J = 6.7 Hz, 1H), 3.72 (d, J = 11.4 Hz, 2H), 2.72 (t, J = 12.0 Hz, 2H), 2.66–2.55 (m, 4H), 2.41 (t, J = 10.2 Hz, 1H), 2.00 (d, J = 9.9 Hz, 2H), 1.84 (d, J = 6.7 Hz, 3H), 1.75 (d, J = 11.1 Hz, 2H), 1.70–1.57 (m, 4H), 1.51–1.47 (m, 2H). HRMS (EI+) m/z calcd for C31H33Cl2N7O 589.2124; found 589.2121.

5-(1-(3,5-Dichloropyridin-4-yl)ethoxy)-3-(5-((3S,5R)-3,5-dimethylpiperazin-1-yl)-1Hbenzo[d]imidazol-2-yl)-1H-indazole (21b). The title compound was prepared from 40b following 35


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general procedure B. Yellow solid (44%), mp 182–183 °C. 1H NMR (300 MHz, CD3OD) δ 8.43 (s, 2H), 7.82 (s, 1H), 7.59 (s, 1H), 7.47 (d, J = 9.2 Hz, 1H), 7.26–7.14 (m, 2H), 7.09 (d, J = 8.9 Hz, 1H), 6.23 (q, J = 6.5 Hz, 1H), 3.62 (d, J = 11.3 Hz, 2H), 3.28–3.13 (m, 2H), 2.45 (t, J = 11.4 Hz, 2H), 1.83 (d, J = 6.6 Hz, 3H), 1.25 (d, J = 6.4 Hz, 6H). HRMS (EI+) m/z calcd for C27H27Cl2N7O 535.1654; found 535.1647.

5-(1-(3,5-Dichloropyridin-4-yl)ethoxy)-3-(5-(4-methylpiperazin-1-yl)-1H-benzo[d]imidazol-2-yl)1H-indazole (21c). The title compound was prepared from 40c following general procedure B. Beige solid (68%), mp 190 °C dec. 1H NMR (300 MHz, CD3OD) δ 8.41 (s, 2H), 7.82 (s, 1H), 7.57 (d, J = 8.7 Hz, 1H), 7.46 (d, J = 9.0 Hz, 1H), 7.21–7.13 (m, 2H), 7.05 (d, J = 8.8 Hz, 1H), 6.21 (q, J = 6.7 Hz, 1H), 3.29–3.21 (m, 4H), 2.82–2.71 (m, 4H), 2.44 (s, 3H), 1.81 (d, J = 6.6 Hz, 3H).

13

C NMR (101 MHz,

acetone-d6) δ 153.3, 149.7 (2C), 145.2, 140.3, 138.5, 137.4, 135.1, 132.0 (2C), 122.7, 120.3, 120.5, 114.8, 112.3, 105.1, 98.9, 72.9, 55.8 (2C), 51.1 (2C), 45.9, 19.0. HRMS (EI+) m/z calcd for C26H25Cl2N7O 521.1498; found 521.1493.

5-(1-(3,5-Dichloropyridin-4-yl)ethoxy)-3-(5-(4-ethylpiperazin-1-yl)-1H-benzo[d]imidazol-2-yl)1H-indazole (21d). The title compound was prepared from 40d following general procedure B. Yellow solid (58%), mp 185–186 °C. 1H NMR (300 MHz, CD3OD) δ 8.43 (s, 2H), 7.82 (s, 1H), 7.62 (s, 1H), 7.48 (d, J = 8.9 Hz, 1H), 7.22–7.04 (m, 3H), 6.24 (q, J = 6.7 Hz, 1H), 3.30–3.23 (m, 4H), 2.78–2.67 (m, 4H), 2.55 (q, J = 7.3 Hz, 2H), 1.84 (d, J = 6.6 Hz, 3H), 1.18 (t, J = 7.2 Hz, 3H). HRMS (EI+) m/z calcd for C27H27Cl2N7O 535.1654; found 535.1651.

4-(2-(5-(1-(3,5-Dichloropyridin-4-yl)ethoxy)-1H-indazol-3-yl)-1H-benzo[d]imidazol-5yl)morpholine (21e). The title compound was prepared from 40e following general procedure B. Beige solid (52%), mp 185 °C dec. 1H NMR (300 MHz, acetone-d6) δ 12.51 (s, 1H), 8.51 (s, 2H), 8.04 (d, J = 2.2 Hz, 1H), 7.62 (d, J = 8.6 Hz, 1H), 7.53 (d, J = 9.0 Hz, 1H), 7.24–7.14 (m, 2H), 7.05 (dd, J = 8.8, 1.8 36



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Hz, 1H), 6.20 (q, J = 6.5 Hz, 1H), 3.88–3.79 (m, 4H), 3.21–3.13 (m, 4H), 1.84 (d, J = 6.6 Hz, 3H). HRMS (EI+) m/z calcd for C25H22Cl2N6O2 508.1181; found 508.1179.

5-(1-(3,5-Dichloropyridin-4-yl)ethoxy)-3-(5-(4-methyl-1,4-diazepan-1-yl)-1H-benzo[d]imidazol2-yl)-1H-indazole (21f). The title compound was prepared from 40f following general procedure B. Yellow solid (57%), mp 145–147 °C. 1H NMR (300 MHz, CD3OD) δ 8.41 (s, 2H), 7.82 (s, 1H), 7.60– 7.42 (m, 2H), 7.15 (d, J = 9.0 Hz, 1H), 6.93–6.78 (m, 2H), 6.21 (q, J = 6.7 Hz, 1H), 3.70–3.61 (m, 2H), 3.54 (t, J = 6.2 Hz, 2H), 2.93–2.85 (m, 2H), 2.77–2.69 (m, 2H), 2.45 (s, 3H), 2.16–2.04 (m, 2H), 1.81 (d, J = 6.6 Hz, 3H). HRMS (EI+) m/z calcd for C27H27Cl2N7O 535.1654; found 535.1650. N1-(2-(5-(1-(3,5-Dichloropyridin-4-yl)ethoxy)-1H-indazol-3-yl)-1H-benzo[d]imidazol-5-yl)-N2,N2dimethylethane-1,2-diamine (21g). The title compound was prepared from 40g following general procedure B. Yellow solid (48%), mp 140–142 °C. 1H NMR (300 MHz, CD3OD) δ 8.42 (s, 2H), 7.80 (s, 1H), 7.54–7.41 (m, 2H), 7.15 (d, J = 10.1 Hz, 1H), 6.81 (s, 1H), 6.73 (d, J = 8.7 Hz, 1H), 6.22 (q, J = 6.6 Hz, 1H), 3.30 (t, J =6.3 Hz, 2H), 2.64 (t, J = 6.3 Hz, 2H), 2.33 (s, 6H), 1.82 (d, J = 6.7 Hz, 3H). HRMS (EI+) m/z calcd for C25H25Cl2N7O 509.1498; found 509.1503.

2-(5-(1-(3,5-Dichloropyridin-4-yl)ethoxy)-1H-indazol-3-yl)-N-(2-methoxyethyl)-1Hbenzo[d]imidazol-5-amine (21h). The title compound was prepared from 40h following general procedure B. Yellow solid (55%), mp 132–133 °C. 1H NMR (300 MHz, CD3OD) δ 8.42 (s, 2H), 7.80 (d, J = 1.8 Hz, 1H), 7.51–7.40 (m, 2H), 7.15 (dd, J = 9.0, 2.1 Hz, 1H), 6.85 (s, 1H), 6.76 (dd, J = 8.7, 1.8 Hz, 1H), 6.22 (q, J = 6.7 Hz, 1H), 3.64 (t, J = 5.4 Hz, 2H), 3.40 (s, 3H), 3.34 (t, J = 5.4 Hz, 2H), 1.82 (d, J = 6.6 Hz, 3H). HRMS (EI+) m/z calcd for C24H22Cl2N6O2 496.1181; found 496.1171.

37


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2-(2-(5-(1-(3,5-Dichloropyridin-4-yl)ethoxy)-1H-indazol-3-yl)-1H-benzo[d]imidazol-5-yl)ethan-1ol (22). The title compound was prepared from 41 following general procedure B. White solid (77%), mp 150–151 °C. 1H NMR (300 MHz, CD3OD) δ 8.42 (s, 2H), 7.82 (d, J = 2.2 Hz, 1H), 7.59 (s, 1H), 7.55–7.44 (m, 2H), 7.21–7.13 (m, 2H), 6.23 (q, J = 6.7 Hz, 1H), 3.84 (t, J = 7.1 Hz, 2H), 3.35 (s, 1H), 2.98 (t, J = 7.1 Hz, 2H), 1.82 (d, J = 6.7 Hz, 3H).

13

C NMR (126 MHz, CD3OD) δ 154.1, 149.8 (2C),

148.8, 146.3, 139.1, 136.8, 135.0, 132.7 (2C), 125.0, 122.8, 120.9, 119.4, 112.5, 104.9, 73.7, 64.8, 40.6, 18.9. HRMS (EI+) m/z calcd for C23H19Cl2N5O2 467.0916; found 467.0918.

General procedure C: Synthesis of ethers 24a–e and 32a–c. 5-Hydroxyindole (1.1 mmol) and cesium carbonate (1.2 mmol) in N,N-dimethylformamide (10 mL) was heated to 70 °C. Benzyl chloride (23a–e) or methanesulfonate (31a–c) (1 mmol) was added and the mixture was stirred for 2 h. Water was added and the reaction mixture was partitioned between ethyl acetate and water. The organic layer was washed with water and brine successively, dried over anhydrous sodium sulfate, and concentrated in vacuum. The resulting residue was purified by silica gel chromatography (petroleum ether/ethyl acetate, v/v, 90:10) to give the desired product.

General procedure D: Synthesis of aldehydes 25a–e and 33a–c. 5-Substituted indole (24a–e, 32a– c) (0.58 mmol) was dissolved in water (6 mL) and dioxane (6 mL). Sodium nitrite (5.8 mmol) was added and the solution was cooled to 0 °C. Hydrochloric acid (3 mL, 3 N) was added dropwise over 5 min and the resulting mixture was then stirred at room temperature for additional 3 h. Ethyl acetate was added and the reaction mixture was partitioned between ethyl acetate and water. The organic layer was washed with water and brine successively, dried over anhydrous sodium sulfate, and concentrated in vacuum.

The

resulting

residue

was

purified

by

silica

ether/dichloromethane, v/v, 90:10) to give the desired product.34 38


gel

chromatography

(petroleum


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General procedure E: Synthesis of substituted 2-nitroanilines 26d, 27 and 40a–h. A mixture of 5fluoro-2-nitroaniline (26a) (468 mg, 3 mmol), N,N-diisopropylethylamine (1.4 mL, 7.5 mmol) and nucleophiles in N-methyl-2-pyrrolidone (20 mL) was heated to 120 °C for 4 h. The reaction mixture was poured into water and extracted with ethyl acetate. The organic layer was washed with water and brine successively, dried over anhydrous sodium sulfate, and concentrated in vacuum. The resulting residue was purified by silica gel chromatography (dichloromethane/methanol, v/v, 97:3) to give the desired product.

Chiral synthesis of (R)-21c Step 1: (S)-1-(3,5-dichloropyridin-4-yl)ethan-1-ol ((S)-30a). A mixture of 30a (3.6 g, 18.8 mmol), (R)-2-(2,4-dichlorophenoxy)propanoic acid42 (42) (2.2 g, 9.4 mmol), and 4-dimethylaminopyridine (114 mg, 0.94 mmol) was dissolved in anhydrous toluene (100 mL). Dicyclohexylcarbodiimide (1.94 g, 9.4 mmol) was added slowly to the mixture at 0 °C. The resulting slurry was stirred at ambient temperature for 20 min and filtered. The filtrate was concentrated in vacuum and purified by silica gel chromatography (petroleum ether/ethyl acetate, v/v, 95:5) to give the corresponding ester as a pale yellow oil (3.8 g, 49%). The resulting ester was dissolved in ethanol (40 mL) and aqueous sodium hydroxide (24 mL, 2 N) was added. The reaction mixture was stirred at ambient temperature for 2 h, then the solvent was evaporated in vacuum. The mixture was partitioned between water and dichloromethane. The organic layer was washed with brine, dried over anhydrous sodium sulfate, and concentrated in vacuum to give (S)-30a’ as a colorless oil (1.75 g, 98%). The aqueous layer was acidified to pH=2 with 2 N HCl and filtered, the filter cake was collected and dried to retrieve 42 as a white solid (2.1 g, 98%). The above mentioned method was repeated once to give (S)-30a as a colorless oil (830 mg, 23% for two steps). [α]20D = +12.07 (c 0.340, methanol) (98% ee, CHIRALPAK AD-H, n-

39


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Heptane: EtOH=90: 10, flow rate 1.0 mL/min, tR= 10.1 min, peak 2)36. 1H NMR (300 MHz, CDCl3) δ 8.44 (s, 2H), 5.59–5.46 (m, 1H), 2.82 (d, J = 9.6 Hz, 1H), 1.63 (d, J = 7.8 Hz, 3H). Step 2: (S)-1-(3,5-dichloropyridin-4-yl)ethyl methanesulfonate ((S)-31a). Compound (S)-30a (800 mg, 4.2 mmol) and triethylamine (0.88 mL, 6.2 mmol) were dissolved in anhydrous dichloromethane (20 mL). Methanesulfonyl chloride (0.5 mL, 6.2 mmol) was added dropwise at 0 °C. After the addition was complete, the resulting mixture was stirred at room temperature for 2 h. Water was added and the reaction mixture was partitioned between dichloromethane and water. The organic layer was washed with water and brine successively, dried over anhydrous sodium sulfate, and concentrated in vacuum to give the title product as a white solid (1.1 g, 95%). Mp: 46–48 °C. [α]20D = −40.06 (c 0.304, methanol). 1

H NMR (300 MHz, CDCl3) δ 8.51 (s, 2H), 6.36 (q, J = 6.9 Hz, 1H), 2.97 (s, 3H), 1.81 (d, J = 6.9 Hz,

3H). Step 3: (R)-5-(1-(3,5-dichloropyridin-4-yl)ethoxy)-1H-indole ((R)-32a). The title compound was prepared from (S)-31a following general procedure C. Colorless oil (85%). [α]20D = +47.66 (c 0.107, methanol) (89% ee, CHIRALPAK AD-H, n-Hexane: i-prOH=90: 10, flow rate 1.0 mL/min, tR= 18.8 min). 1H NMR (400 MHz, CDCl3) δ 8.40 (s, 2H), 8.11 (s, 1H), 7.23 (d, J = 8.8 Hz, 1H), 7.14 (t, J = 2.8 Hz, 1H), 6.99 (d, J = 2.4 Hz, 1H), 6.88 (dd, J = 8.8, 2.4 Hz, 1H), 6.41–6.39 (m, 1H), 6.02 (q, J = 6.7 Hz, 1H), 1.79 (d, J = 6.7 Hz, 3H). Step 4: (R)-5-(1-(3,5-dichloropyridin-4-yl)ethoxy)-1H-indazole-3-carbaldehyde ((R)-33a). The title compound was prepared from (R)-32a following general procedure D. The obtained solid was suspended in ethyl acetate and stirred for 30 min. The slurry was filtered and the filter cake was dried in vacuum to give (R)-33a. Yellow solid (55%). Mp: 188 °C dec. [α]20D = +76.33 (c 0.207, methanol) (99% ee, CHIRALPAK AD-H, n-Hexane: i-prOH=90: 10, flow rate 1.0 mL/min, tR= 18.2 min). 1H NMR (300

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MHz, CDCl3) δ 10.13 (s, 1H), 8.37 (s, 2H), 7.52 (s, 1H), 7.41 (d, J = 9.0 Hz, 1H), 7.13 (d, J = 9.1 Hz, 1H), 6.07 (q, J = 6.7 Hz, 1H), 1.78 (d, J = 6.7 Hz, 3H). Step

5:

(R)-5-(1-(3,5-dichloropyridin-4-yl)ethoxy)-3-(5-(4-methylpiperazin-1-yl)-1H-

benzo[d]imidazol-2-yl)-1H-indazole ((R)-21c). The title compound was prepared from (R)-33a following general procedure B. Pale yellow solid (62%). Mp: 199 °C dec. [α]20D = +229.29 (c 0.218, methanol) (99% ee, CHIRALPAK IE, n-Hexane: EtOH: diethylamine =70: 30: 0.1 (v/v/v), flow rate 0.8 mL/min, tR= 20.7 min). 1H NMR (300 MHz, CD3OD) δ 8.41 (s, 2H), 7.82 (s, 1H), 7.57 (d, J = 8.7 Hz, 1H), 7.46 (d, J = 9.0 Hz, 1H), 7.21–7.13 (m, 2H), 7.05 (d, J = 8.8 Hz, 1H), 6.21 (q, J = 6.7 Hz, 1H), 3.29–3.21 (m, 4H), 2.82–2.71 (m, 4H), 2.44 (s, 3H), 1.81 (d, J = 6.6 Hz, 3H).

13

C NMR (101 MHz,

acetone-d6) δ 153.3, 149.7 (2C), 145.2, 140.3, 138.5, 137.4, 135.1, 132.0 (2C), 122.7, 120.3, 120.5, 114.8, 112.3, 105.1, 98.9, 72.9, 55.8 (2C), 51.1 (2C), 45.9, 19.0. HRMS (EI+) m/z calcd for C26H25Cl2N7O 521.1498; found 521.1493.

Kinase profiling The kinase profiling of (R)-21c was conducted using Elisa kinase assay and the Eurofins Kinase Profiler Selectivity Testing Service. Elisa kinase assay: The effects of indicated compounds on the activities of various tyrosine kinases were determined using enzyme-linked immunosorbent assays (ELISAs) with purified recombinant proteins. Briefly, 20 µg/mL poly (Glu, Tyr) 4:1 (Sigma, St Louis, MO, USA) was pre-coated in 96-well plates as a substrate. A 50-µL aliquot of 10 µM ATP solution diluted in kinase reaction buffer (50 mM HEPES [pH 7.4], 50 mM MgCl2, 0.5 mM MnCl2, 0.2 mM Na3VO4, and 1 mM DTT) was added to each well; 1 µL of various concentrations of indicated compounds diluted in 1% DMSO (v/v) (Sigma, St Louis, MO, USA) were then added to each reaction well. DMSO (1%, v/v) was used as the negative 41


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control. The kinase reaction was initiated by the addition of purified tyrosine kinase proteins (FGFR1, FGFR2, FGFR3, FGFR4, VEGFR2, EGFR, ErbB2, PDGFRα, PDGFRβ, c-Met, Flt1, Flt3, RET , c-Src ,Bcr-Abl

and EPHA2) diluted in 49 µL of kinase reaction buffer. After incubation for 60 min at 37 °C, the plate was washed for three times with phosphate-buffered saline (PBS) containing 0.1% Tween 20 (T-PBS). Anti-phosphotyrosine (PY99) antibody (100 µL; 1:500, diluted in 5 mg/mL BSA T-PBS) was then added. After a 30-min incubation at 37 °C, the plate was washed for three times, and 100 µL horseradish peroxidase-conjugated goat anti-mouse IgG (1:1000, diluted in 5 mg/mL BSA T-PBS) was added. The plate was then incubated at 37 °C for 30 min and washed for three times. A 100-µL aliquot of a solution containing 0.03% H2O2 and 2 mg/mL o-phenylenediamine in 0.1 M citrate buffer (pH 5.5) was added. The reaction was terminated by the addition of 50 µL of 2 M H2SO4 as the color changed, and the plate was analyzed using a multi-well spectrophotometer (SpectraMAX190, from Molecular Devices, Palo Alto, CA, USA) at 490 nm. The inhibition rate (%) was calculated using the following equation: [1(A490/A490 control)] ×100%. The IC50 values were calculated from the inhibition curves in two independent experiments. The activity of (R)-21c, at a concentration of 100 nM using an ATP concentration of 10 µM, was screened against a panel of other 43 human protein kinases by Eurofins using the Eurofins Kinase Profiler Selectivity Testing Service.

Cell culture The human lung cancer cell line NCI-H1581, human acute myelogenous leukemia cancer cell line KG-1, and human gastric cancer cell line SNU-16 were purchased from American Type Culture Collection (ATCC, Manassas, VA, USA); human bladder cancer cell line RT112 was purchased from

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DSMZ-German collection of microorganisms and cell cultures. All the cell lines were routinely maintained in media according to the suppliers’ recommendations.

Cell proliferation assay Cells were seeded in 96-well cell culture plates. On the day when seeding, the cells were exposed to various concentrations of compounds and further cultured for 72 h at 37 °C. Cell proliferation was then determined using Cell Counts Kit-8 (CCK8,) or the thiazolyl blue tetrazolium bromide (MTT, from Sigma-Aldrich, St.Louis, MO, USA) assay. The IC50 values were calculated by concentration-response curve fitting using the four-parameter method.

Statistical analysis Data from the in vitro assays are presented as the mean ± SD. The statistical difference between multiple treatments and controls was analyzed using Student’s t test. P

1H-indazoles as Potent Fibroblast Growth Factor ... - ACS Publications

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